The Truth Is Out There And It Hurts
by Dana'sFairytales
Summary: Emily wasn't the only child Scully bore when she was abducted. When Scully goes missing, Mulder must rely on Holly, Scully's Daughter, to help find her. However time is running out for Scully, and Holly seems to be creating more questions, than she is answering.
1. Chapter 1

Scully lies asleep in a double bed, the covers beside her have been slept in. She rolls over and wakes. Slowly she sits up, looking around the room; reaching over and turns on the light.

"Mulder?"

Scully flings her legs over the side of the bed, stretches and then gets up, walking through to the kitchen.

"Mulder, where are you?"

Scully fills the kettle, and turns it on, leaning on the worktop.

Scully jumps at the sound of someone knocking on the door. Scully looks at the clock, 2:17, she heads to the door, and opens it to three men in black suits.

"Can I help you?"

"Yes, are you Dana Scully?"

"That depends on whose asking."

The man in front turns to look at the other men. Scully starts closing the door, the man pushes hard against the door. Scully tries to keep the door closed, but all three men push, sending her flying back. Scully begins to run into the apartment, followed closely by the men.

"Help, somebody help me." Scully screams

One of the men grabs her, pulling her back from the phone she was almost touching. One of the others takes a bottle and handkerchief out of his pocket. Pouring some liquid onto the handkerchief, he puts it over her mouth and nose. Scully continues struggling, and then goes limp in his arms.

"Leave the handkerchief, make it clear there was a struggle, I'll get in her in the car"

The man lifts her and carries her out the apartment, as the others knock over furniture. One takes a vile of blood out his pocket and pours it onto the carpet.

The two men leave, the door is left ajar, the elevator sounds just as the kettle boils.

Mulder walks down the corridor carrying a paper bag and two coffee cups. Skinner appears through the door, as he gets half way.

"Skinman! You and Scully not getting it on are you?"

"Mulder, I….."

Crime scene investigators exit, and walk past Mulder.

"What happened? Where is she?"

Mulder runs into the apartment, Skinner comes after him, and grabs him by the shoulders.

"We don't know where she is, who ever took her used Chloroform, and there was defiantly a struggle."

Mulder sits on the sofa, face in hands.

"Has anyone threatened you?"

"No, not her, I had a run in with some guys involved in a government plot, but….I can't believe, not because of me."

"We'll find her."

"You're retiring soon."

Both turn at a knock on the door, a girl, 18 nearly 19 stands there, she tilts her head round the door. "Hello?"

"This is a crime scene, you can't be here" skinner walks over to her and they go into the corridor, Mulder sighs, and follows.

"I just need to talk to him."

Mulder walks out into the hall.

"You'll talk to me won't you?" she pushes past Skinner, and goes to Mulder.

"What do you want?" Mulder sighs

"I know who took her, and I need to find her."

"Who? Who took her?"

"The men you pissed off. They want to make you suffer."

Mulder pushes her against the wall.

"Who are you? Are you involved with them?"

"Mulder." Skinner puts his hand on his shoulder.

The girl pushes Mulder back and starts walking towards the elevator.

"Wait, I'm sorry, can you help me find her?" Mulder calls to her.

She stops and turns.

"Apology accepted. I'm Holly; I can help you find her. I need to find her myself"

"Who are you?"

"I'm Scully's daughter. I'm Emily's sister"


	2. Chapter 2

Scully lies on her side, on a metal operating table, her hands are tied behind her back. Her eyes flicker as a large light turns on above.

Two men and a women enter, their faces hidden by surgical masks, the woman pushes a tray of surgical instruments. They gather round. The door is heard opening.

"Sorry you can't smoke in here." One man turns, the others continue with their preparation.

Coughing is heard, then the sound of the door opening and closing again.

"Right let's get started"

Mulder and Holly sit in a café; there is an untouched coffee and piece of pie in front of him. She sits drinking diet coke.

"You said I was wrong how can you be sure?"

"Your case was heavily pregnant women turning up in hospitals, and there was no ID and no record of them. Am I right?"

"Yes."

"It was no conspiracy; they were prostitutes from foreign countries. They were not abductees."

Mulder pulls his coffee close, remaining silent staring into the black liquid.

"It's cold, would you like another?"

"No, I want to know where Scully is."

"I don't know"

Mulder stands up.

"Then what is the point of me even talking to you, I could be finding her."

He starts to leave, throwing some change onto the table; she quickly follows, nervously glancing at the other customers, as they stare.

Holly catches up with him on the street.

"I don't know where she is, but I think I know who has her, and I think I can help you find her."

Mulder stops.

"We need to go somewhere safe, there I'll tell you everything I know"

Holly motions to Mulder's car, unlocking it they climb in.

"Where to?"

"Just drive."

The car pulls away, a man in a suit on the pavement, touches his ear.

"They are leaving, please advise if I should pursue or not."

The man nods, and then walks away down the street.

Mulder and Holly sit silently in the car.

"Are you going to tell me?"

Holly sighs and looks out the window.

"I don't want you to crash the car in anger."

She smiles.

"Emily wasn't the only one born; there were 12 of us…"

"Twelve! You mean there are ten more of you?"

"No, it's just me now. The other died some like Emily, others killed."

Holly wipes a tear away.

"I'm sorry."

"It's ok, I never knew them. You never realised this but they always make multiple children, with different mutations, but they kill them off before they reach double digits."

"How come you survived?"

"I was saved by my dad, after you found Emily, they panicked, terminate the project early."

Mulder pulls in at a gas station, and climbs out.

Holly gets out, and heads to the bathroom. Mulder waits until the door closes then pulls out his mobile.

"Hey Skinner."

"Where are you?"

"Just on a little road trip with Holly."

"All the blood in the apartment was Scully's there is no DNA evidence from her abductors. You know where she is?"

"No, I'm starting to think this might be a wild goose trip."

"I'll do everything I can, but be careful. Mulder I mean it."

"Of course skinman, I'll keep you updated."

Mulder hangs up, and fills the car. Holly comes out the bathroom and goes straight into the shop. Mulder sits in the car; she comes out carrying two bottles of water and a packet of M&Ms.

"Ready?"

"Yeh, just a quick question, where you get all this money?"

"I stole it from dad before I left. Off we go."

Holly smiles at the dumbstruck Mulder.


	3. Chapter 3

Skinner sits at his desk frowning down at a piece of paper.

"How long till he calls?"

A young man stands in the corner, smoking.

"I don't know, he just said he'd keep me updated, I have no control over his actions."

Skinner turns the page; the man walks over and puts out his cigarette on tissue.

"Only a few weeks till retirement, you'll want to make them ones to remember."

The man smiles and leaves.

Skinner closes the file, and takes out of his drawer an old mobile. He dials.

"Mulder, you need to move fast, they are coming up close behind you," Skinner whispers, then hangs up.

Skinner stands and walks calmly over to the window, wiping the phone with a tissue he throws it out, along with the man's cigarette. Skinner sits back down and looks at the file; it has a large X on it. Opening it, there is a picture of Dana Scully, in hospital after she was abducted.

Skinner closes his eyes, and takes off his glasses, rubbing his temple.

"Sir?"

Skinner opens his eyes, to see his secretary standing by him.

"Yes, what is it?" Skinner sighs, standing up and pulling on his jacket.

His secretary hands him a packet.

"I found this in one of my drawers."

His secretary forces a smile, then turns and leaves.

Skinner turns over the packet, then takes his letter opener and carefully opens the envelope. He tips it upside down on his desk.

Out falls a gold chain with a small gold cross, and a folded note. Skinner picks up the necklace, and puts it in his pocket. He then unfolds the note.

"Kelly's Bar. 9pm."

Skinner tears up the note, putting the pieces in his pocket, collecting the rest of his things, he turns of his desk light and leaves.

XXX

Kelly's Bar sits in the corner of an otherwise run down street. A group of men stand outside, the look suspiciously as two men walk towards them.

Mulder and Skinner part to get past the men, revealing Holly. The men smile at her, and one wolf whistles.

The three manage to get in, and sit at a round table, near the back. Skinner goes to the bar leaving Holly and Mulder alone.

"Why do you dislike me so much?" Holly leans over the table

"I don't dislike you, I just don't know if I trust you, or believe your story."

Holly leans back.

"I moved to England with my dad when I was about four. The syndetic, were getting rid of rest of us, but my father couldn't stand to let me die. So we ran. He wasn't my real dad; he was the scientist in charge of me. Unlike Emily most of us never left a lab."

Skinner returns, and hands Holly, a coke, and Mulder a beer. He sits down with a glass of water.

"Not drinking?"

"No."

The three sit in awkward silence, occasionally drinking.

A woman in a black suit walks over to the table.

"Mind if I join you?"

Mulder looks at her, eyes burning in hatred.

"No, course."

Skinner slides round allowing her to perch herself at the edge of the seat. Holly stares down into her drink. Mulder keeps his eyes on her. She looks round, surveying the scene and each of them individually.

"Well, I am Dr Foster, Holly I am sure as told you all sorts of horror stories about me and my organisation. But they are I assure you, just the delusions of her sick father. Now….."

"They were not!"

Holly, hisses under her breath.

"You killed him, you tried to kill me, and now you're hurting Scully…."

"Calm down dear, there is no point getting worked up, perhaps you should leave us adults to discuss the situation, which you clearly do not understand."

Holly sits still, glaring at Dr Foster.

"So you are going to behave yourself, good. Now to business, I personally do not know where Dana Katherine Scully is. But...only I can ensure her safe return. Understand so far?"

"No, explain to me why, you took her?" Mulder says, trying hard to control the anger in his voice.

"Firstly I did not take her. Secondly I am getting to that. Skinner would you mind getting me a drink, water with lemon no ice. Perhaps Holly will accompany you."

Skinner nods, Dr Foster stands allowing Skinner and Holly to walk to the bar. Dr foster sits by Mulder.

"I can help you get her back, but you need to trust me. This isn't your fault. They took her because of Holly. I don't know what she has told you, but Holly is on the run, for murdering her father. They took Scully to lure her to them. Instead she found you."

Mulder turns to look at Holly, she sits on a bar stool, spinning round as Skinner talks to her.

"I don't trust you, and if you want me to hand her over to you, you can forget it."

"I thought you'd have a little difficulty with it." She's takes a phone out of her pocket, and presses the call button.

"Now I didn't want to do this, but I feel I just need to remind you what's at stake."

Dr Foster hands the phone to Mulder; he takes it and holds it to his ear.

"Fox Mulder?" a metallic voice says

"Yes…"

There is a piercing beep.

"Mulder, are you there?" Scully says

"God, Scully are you alright? Where are you? I've been so worried and….."

Scully is heard crying

"Mulder, they put something in me, it hurts so much and….."

A scream is heard.

"Scully? Scully? Talk to me? Scully?"

The phone goes dead. Mulder drops it on the table, and looks at Dr Foster.

Skinner and Holly return at that moment.

"Thank you, I must be on my way."

Dr Foster stands and starts to walk away. She stops as she goes past Mulder and puts her hand on his arm.

"You know what you need to do."

Dr Foster smiles at them.

"Holly."

"Dr Foster"

The two nod at each other, and Dr Foster leaves. Holly turns to look at Mulder.

"What did she mean by that?"


	4. Chapter 4

XXX

Scully sits unconscious, in a small dark room with no windows, wearing a hospital robe. She wakes and stands stretching. She peers at her arm, where needle marks are visible.

A slot opens at the bottom of the door and a tray of food and a bottle of water are pushed in. Scully picks it up and looks around, she then sighs and sits down on the floor.

XXX

Holly stands outside the pub smoking. Mulder comes out and stands beside her. Skinner walks past them, to the car, and begins to make a phone call.

"I need to know the truth." Mulder turns to her.

Holly drops her cigarette, and stamps it out.

"The truth hurts, Mr Mulder."

Mulder turns away.

"I'm not sure you can cope with the truth."

"I can anything for her."

Holly looks into his eyes and smiles.

"Okay. We came here a few months ago, me and my dad; we've been living in hiding. I don't know why but they suddenly after all these years started coming after us."

Holly turns and starts to walk off, then turns back frustrated.

"This is your entire fucking fault!"

"My fault, how is it my fault?"

"They took her originally to punish you, if you'd looked after her, kept her safe, none of this would have ever happened!"

Mulder turns his head, and looks at the ground.

"I feel guilty every day for what I've lead her into, for what's been taken from her, but I can't change the past, if I could I'd do it in a heartbeat."

"I'm sorry; I forget that you've suffered to."

The two stand in silence and Skinner walks over.

"What's wrong?" he asks worried.

"Nothing, look Dr Foster wanted us to hand you over in return for Scully. That isn't an option; we need to find everything we can about her." Mulder and Skinner begin walking to the car.

"Let them take me."

"What?" Mulder turns.

"Look, it makes sense, I have nothing left, and they created me. I want to do something good. Mulder?" Holly looks into his eyes, he can't meet her gaze, and her eyes look so similar to Scully's.

"Who is Dr Foster?" Skinner interrupts.

"She is the one who kills us. Makes us disappear from all records, makes sure that no one ever knows we existed. She looks after you, doing tests for the month before you are terminated."

Mulder shifts uncomfortably.

Skinner "How do you know this?"

"My dad told me, he has files on all the kids they did this to."

"Did?"

"Yes, the project has stopped now, I'm the only lose end."

"Right." Skinner nods, "Let's get going."

Skinner walks to the car and gets in leaving Mulder and Holly.

"I can't give you up. Scully would spend eternity looking for you."

"If you don't, I'll never tell you about William."

Mulder stares at her, aghast.

"Come on, you heard skinman time to go."

Holly runs off and climbs into the back of the car.

Mulder stands for a few seconds, and then also climbs into the car. As the car drives off, Dr Foster comes out of the shadows, with the man who was in Skinner's office, who is smoking.

"She's a good little liar isn't she?" he smirks

"She was trained well."

"Hmm, but will it work."

"Yes, I think we'll get everything we want."

A long black car pulls up in front of them. The man stamps out his cigarette.

"She better get the job done, or you'll both pay for it."

He gets in. The car pulls away leaving Dr Foster alone.

XXX

Scully sits in the cell, she is looking around, a small lamp is now with her, and it provides an orange glow. She notices a small hole in the wall, and crawls over to it, lying on her belly to pear through.

It looks through into another cell where a middle age man sits, rocking back and forth.

"Hello?" she calls out

The man laughs.

"So they got you too did they?"

The man suddenly crawls very quickly right up to the hole. He chuckles.

"You bitch. Mother of a monster. Creator of demons."

"What are you talking about?"

"oh don't worry you'll see soon enough."

"But…"

A bang on the door interrupts her, Scully turns to see.

"No talking" a stern voice says.

Scully looks back through the whole, but the man is back in his initial position. Scully leans back and lets her eyes close.


	5. Chapter 5

Love to hear your theories! x

Mulder sits alone in the apartment, reading through files, and suffering the internet. It is dark except for one small desk light. There is a knock at the door, taking a swig of beer from the bottle he walks over and looks through the peep hole. There stands Skinner. Mulder sighs and pulls the door open.

"Evening Mulder." Skinner walks in holding an envelope.

He hands it to Mulder, who stares at it, then slams the door, and goes back to sitting on the sofa. Skinner walks over and turns on the light switch.

Mulder dips the contents of the envelope onto the table. It is a Polaroid photo. He picks up the photo; it shows Holly, Dr Foster, the man who smokes, and the man in the cell beside Scully. All are smiling a barbeque can be seen in the background.

"Who are all these people?" Mulder asks, looking up at Skinner.

"Dr Foster, is a biologist working out of Li-Cor, she recently spent time in the UK, the man smoking is paid by the Syndicate, he has influence within the FBI, and many other places of power, the man is a scientist, he has been missing for several days, and living in the UK, for what I can gather he is Holly's father."

Mulder throws the photo down and rubs his head.

"None of this makes any sense. I mean why take Scully to get Holly? Why drag you and me into it?"

"To distract us, and you missed the most important question. Who is Holly?"

"You don't believe her story?"

"It has too many gaps, unexplained things. I have looked and she doesn't exist. She doesn't even own a mobile. And another thing whose sending me these letters?"

"I don't know, I'll talk to you tomorrow."

Skinner nods and makes his way to the door alone. He suddenly stops and goes back; he takes Scully's necklace out his pocket and lays it on the table in front of Mulder. He then turns of the lights and leaves.

Mulder sits alone in the dark, then picks up the necklace, closing his hand into a fist, he moves it up to his mouth, and begins to cry.

Xxx

Skinner stands outside on the street. A man wearing a cap and hoodie walks past behind him, bumping into him.

Skinner didn't feel the needle, but soon his motor functions are down, a car pulls up in front of him. The man returns and pushes him into the car. Skinner lies on the floor of the car. Dr Foster sits there as does the young man.

"How nice of you to join us." The man smiles

Skinner tries to speak, but only mumbles come out.

"No, no don't try and speak. I believe you know my colleague Henry Strughold." Dr Foster smiles, she then leans down to Skinner.

"Just go to sleep Walter, there is no point fighting. "

Dr Foster removes his glasses, breaks them and throws them out the window.

"Don't worry you'll have a friend to keep you company soon."

Skinner's eyes slowly close. Dr Foster and Sturghold get out the car. Dr Foster taps on the window and it pulls away. Another quickly replaces it.

Strughold climbs in; Dr Foster stays on the pavement, hand s deep in the pockets of her trench coat. She looks up and sees Mulder's window. He appears at the window; she nods at him and then walks off down the street.


	6. Chapter 6

**Please review and let me know what you think! Also was feeling a bit mean whilst writing so no Scully or Skinner. But I promise they will be in next one! x**

Mulder sits asleep on the sofa; there is a blanket over him. The files on the table are all neatly piled. The smell of sausages wakes him from his sleep. He rubs his eyes, the radio is playing soft music, and the kettle is just reaching the boil. Mulder rubs his eyes, and stretches. A look of confusion crosses his face, and he jumps up, and quietly walks to the kitchen door.

He hesitates before he looks in, he wants to see Scully, believe she's home, making him breakfast, singing along to the radio, dancing in a baggy shirt. Of course she'd stop the moment he came in, but he always knew she danced and sang, and he loved to watch. Mulder didn't want to look, what he feared wouldn't be there was too hard to face.

He opened the door there stood Holly, putting sausages into rolls. She is also making a pot of tea.

"What are you doing here? How'd you get in?"

Holly turns and smiles and puts the two plates on the table, and sits down.

"I came to talk to you."

Holly motions to the chair, Mulder sits looking suspiciously at the food and her.

"I can't do it, I can't go with Dr Foster, I thought I could, knowing it would save her, but I can't. I'm Sorry"

Mulder stands up, one hand on his hip, the other touching his forehead. He suddenly throws the dish across the room. Holly jumps but remains sitting. She puts her hand under the table, eyes still focused on Mulder, and pulls up her bag.

Holly puts Skinner's broken glasses on the table. Mulder is leaning against the counter. He turns to see the glasses; he storms over and grabs them.

"Where did you get these?"

"I found them, on the street, this morning, they've taken him too."

Holly stares into Mulder's eyes, as he leans over her. She is visibly scared, Mulder leans back.

"None of this makes any sense!" He shouts slamming his hands down on the table, making all the salt fall over.

Holly jumps and starts to make her way to the door quickly.

Mulder grabs her arm, stopping her.

"Why am I so angry?" he gasps

Holly looks at him, then pulls a Taser out of her bag, and hits him in the stomach. Mulder falls, and lies on the floor.

Holly then runs, leaving the apartment door wide open.

X X X

Holly enters a caravan; it is full of equipment, both old and new. Files cover every other available surface. As well as an empty photo frame, on the floor, Holly steps on this, shattering the glass. She doesn't look down and pushing files off a swivel chair, turns on a laptop.

The screen is black, and then green code begins to appear. Holly picks up a small mobile phone sitting by the laptop, and dials a number.

Holding the phone to her ear with her shoulder, she begins to type code.

"It's me."

"Yes, I know."

"No, it's going to plan."

"Of course I'm not an idiot"

"We'll speak again soon"

"Goodbye."

Holly lets the phone drop. Types a few more lines then throws a few files into a bag, and a photograph. Holly throws the bag outside and then walks into the kitchen area. From under the sink she takes a large canister, and begins pouring petrol everywhere. Holly then turns on the gas stove. Tying a strip of material to the table leg, she drags it outside, and picking up her bag walks till it is tight.

Holly then takes a lighter from her pocket and sets fire to the rag, and begins to run. The caravan explodes, as Holly runs away.


	7. Chapter 7

Dr Foster squats beside Mulder, she slaps him lightly across the face, and he starts up.

"Careful, take it easy."

Mulder slowly stands, and Dr Foster helps him onto a seat.

"What happened?"

"From what I can tell Holly attacked you."

"Why?"

"She's done a runner, I didn't want to tell you this, but I suppose there is no point lying now."

Dr Foster goes makes two glasses of water, then comes and sits with Mulder at the table.

"What haven't you been telling me?"

"Holly isn't Holly, when her and her father came here from Britain; she was replaced by an alien bounty hunter. She's after agent Scully, and your files. That's why we took her to protect her."

"That phone call didn't make it seem like you were protecting her."

"It was faked. Skinner has also been taken to ensure his safety. But you, we need your help."

Mulder looks at her suspiciously, he couldn't trust her, do much didn't make sense, and yet nothing ever seemed to. If Holly was here he could check Dr Foster's claims, but it was too late now, he had to do what this women wanted.

"How?"

"The syndicate isn't the evil conspiracy you once knew, anymore. We are about protecting people. We…."

"Cut the sales pitch, what do you want?"

"We want you to kill an alien bounty hunter, working out of the FBI. He is a killer and trying to destroy everything you worked to build. He's the one that ordered the death of Agent Doggett last spring."

Mulder sighed, he knew Doggett had died seeking a truth, but he had not known what. He thought of all the people he had lost due to this fight, and yet here he was still alive, with hundreds of files that couldn't conclusively prove anything.

"Why can't you kill him?"

"He's expecting us, but you, you're of interest to him. His name is Martin Walsh. Killing him will force "holly" out into the open, and then we can stop her."

Mulder drinks some water. Dr Foster fidgets nervously.

"I'll do it."

Dr Foster's face fills with glee.

"Thank you, everything will be able to come out now, all your work exposed."

Mulder stands and motions to the door, Dr Foster gets up quickly, and walks to the door, Mulder opens it for her but stops her in the doorway.

"Just one thing."

"Yes?"

"Where is Holly?"

Dr Foster looks at her feet.

"The real Holly died in an experimental procedure that was meant to save her life. Believe me when I say, we were close, and I cared greatly for her. That is why what you are going to do is so important. To stop any other children being created to die."

Dr Foster smiles, shakes Mulder's hand and leaves.

Mulder rushes to his laptop, and googles "Martin Walsh"

An article appears dated 2 days ago, "Walsh plans to shake the Bureau to its core, with new policy"

Mulder skims the article, it only says that he is going to be making changes, but there is no clear sign of what these changes are to be.

Mulder sighs and closes the laptop. Wandering over to his desk drawer, from which he pulls a gun, he loads the ammo. And sits at his desk.

X X X

Scully hangs by a chain from the ceiling in a completely white room. Her feet don't touch the floor, a chair and table sit not far from her. Her wrists are bleeding and bruised from struggling. She hangs barely concisions.

Her eyes open, and her head rises at the sound of a bolt being pulled back, slowly the door creaks open, a man in a white lab coat enters, followed by two men who are dragging Skinner.

"No!" Scully screams and start struggling.

The man laughs and walks over to a wheel, he turns and Scully comes closer to the floor, until eventually she is sitting.

Skinner is thrown beside her. And the men all leave.

Skinner is handcuffed, and has a black eye and bleeding lip.

Scully pulls herself close to him.

"Oh Skinner, what are you doing here?" she gasps hugging him, tears fall down her face.

"I'm fine, How are you?" Skinner stretches up.

"I don't understand what's happening."

"I think they want your daughter" Skinner looks at Scully, with great pity.

Scully looks back confused, then suddenly hope spreads across her face.

"Emily is alive? How? I mean what…"

"No." Skinner interrupts "They made more than one child, the one they want is called Holly."

"You've meet her? What is she like?"

"Scully, she's got problems."

Scully closes her eyes and turns her head away.

"I'm so sorry."

"I know, when you said they made more than one, are there more?"

"Not anymore."

Scully sinks off her knees, tears swelling in her eyes.

Skinner moves closer to her, and she rests her head on his shoulder.

The door opens, Skinner's eyes widen as someone walks through.

"No."


	8. Chapter 8

Mulder walks towards the FBI building, his gun in its holster. An ID badge on his pocket, it's out of date, but he knows the man at security.

Mulder manages to walk through with little trouble, he gets in the lift, Walsh is on the 5th floor, Mulder's hand hovers over the button then he presses the button for the basement. Mulder arrived and walked along to a room that used to be his life.

It was empty a desk was still there, his cabinet and a few of his old posters, but it was clear no one used it, we walked over on the desk was Agent Doggett's name.

"What are you doing here?"

Mulder spun to see Agent Reys standing in the doorway, holding an empty cardboard box.

"Mulder?" she gasped, putting the box down and then went and hugged him. Mulder didn't hug her back; she pulled away and looked at him. He noticed the visitor's badge. She notices him staring.

"Oh yeh, they claim I had a mental break down a few years ago, fired me. I'm just here to get Doggett's things. What about you?"

"Oh you know, feeling nostalgic. " Mulder nodded

Reyes turns and stands behind the desk, holding the box.

"I'm glad to see one of us is still able to fight."

"What do you mean?"

"They are trying to destroy us, they killed Doggett, framed his partner, they got me sectioned, and soon skinner will be gone."

Reyes slumps in the chair, scratching her arm, where needle marks are obvious. Mulder nods at her, and turns to leave.

"It was nice seeing you Monica, but I must go now."

Mulder hears her crying and leaves, and goes up to the fifth floor.

He walks along the corridor getting odd looks from those around him. They know who he is. Mulder arrives; Director Walsh's secretary is away, allowing him to walk straight into his office.

Walsh sits with his back to Mulder on the phone. He turns as Mulder lets the door slam shut.

"I'll call you back." He hangs up and rises, hand outstretched to Mulder.

"It's an honour to meet you."

Mulder shakes his hand.

"I must say though I'm confused why you are here. Please sit."

Mulder continues to stand.

"I heard you were looking into the X-Files."

"You're correct; my findings will be published in two days, along with some recommended changes to the Bureau. I'm afraid that's all I can tell you."

Mulder pulls out his gun, Martin Walsh jumps up, hands raised.

"You've got this wrong Mulder. I'm trying to help you."

"Turn around. Now! Up against the window."

Mulder edges behind the Walsh, and with one hand still clutching his gun, pulls back the collar of his shirt, to reveal to lump.

Mulder holsters his gun.

"I'm sorry. I had to check, I was given false information about you."

Mulder backs away, Walsh turns shocked, and shaking.

"By whom?"

The door suddenly flies open; Holly stands there a gun with a silencer in hand. Mulder can see Walsh's secretary lying dead, behind her desk.

Holly slams the door.

"I knew you couldn't do it, Scully's life is on the line, and you still can't do it."

Walsh stares at Holly. Recognition flashes across his face.

"Holly? I thought…."

Holly shoots him through the neck; he falls to the floor, hand reaching out to her.

Mulder rushes to his side, he is still trying to grasp for air, but only for a few seconds, then his eyes glaze.

"Why? He knew you."

"Of course he did, he was one of them, and he helped hurt me and her."

Mulder is walking towards her, anger in his eyes, she backs away.

"I don't think you know what you're talking about. I think someone is feeding you lines, and you have no idea what is going on."

Holly pulls the gun on him. Mulder stops, Holly opens the door eyes still on Mulder, pulls open the door and runs, dropping the gun, on her way.

Mulder looks around; there is nothing he can do. He is torn if staying or leaving is worse. He decides he has to go, otherwise he may never find her. He leaves, trying to look calm.

X X X

Holly is still running, when she ducks into a mall, she goes straight to the toilets. Once having locked the cubicle she closes the lid of the toilet, and sits down. Her head in her hands she begins to cry. Wiping away her tears with the back of her hand, she pulls out a mobile, and dial.

"William, it's me, I need your help."


	9. Chapter 9

**A Short Chapter I Know, But trying to round it all off quite soon! As always please review, and tell me what you theories! x**

Scully lies tied up on the floor, Skinner is unconscious on a chair. He is covered in blood and bruises. Scully struggles against her bindings. She wants to scream out to him, make him wake up, but the gag prevents her.

The door opens; Scully closes her eyes, trying hard to control her breathing. Dr Foster and Henry Strughold enter.

"There is no point pretending Dana." Henry smiles, he leans down, brushing an errant strand of her hair of her face. She flinches at his touch, pulling back, she opens her eyes.

Strughold stands up.

"Don't worry this is all wrapping up now."

Dr Foster walks over to skinner and strikes him across the face. He moans but does not wake, Dr Foster then goes and gets a bucket filled with icy water, and throws it across him, he awakes gasping.

"I thought you'd want to know that Director Martin Walsh is dead."

"What?" Skinner asks confused, trying hard to get his brain to work.

"Mulder has killed Director Walsh, in exchange for you and Dana." Sturghold says coming over to stand by Dr Foster.

"Walsh wasn't a threat."

"Quite the contrary, he planned to release some of the X-Files findings and drive out the corruption within the FBI, and Mr Sturghold here would have been a prime target." Dr Foster smiles

"Now what?" Skinner looks at them

"Now, we clean up." Dr Foster smiles.

She turns and walks to Scully; she grabs her by her hair, and drags her to the door. Scully struggles but her body aches with every movement.

Skinner shouts "No, let her go!"

Dr Foster lets go, letting Scully's head fall and hit the floor, she winces. Dr Foster presses a button, then comes back to Skinner and cuts him off the seat; his hands remain tied behind his back.

Dr Foster points to the door, Skinner walks over and kneels down beside Scully.

3 men walk in, one lifts Scully, placing her over his shoulder. The other two grab Skinner by the arms, and lead them out.

Strughold lights a cigarette.

"This is going all to plan, have you located Holly?" he smiles evilly, putting his hand on her shoulder, she gulps.

"Well no, she torched all of her father's, I mean Dr Taylor's, work. But she was at the FBI with Mulder. But then we lost track of her."

"Strughold pats her shoulder and walks away.

"I think she'll be back here soon."

He drops the cigarette and leaves Dr Foster alone.

Her phone rings and she answers.

"You better have good news for me."

"yes, we tracked the last call she made." The voice says

"Where?"

"She's gone to William."

"William? The idiot girl. This is going to work out perfectly, get a team ready; we'll take them both out."

Dr Foster hangs up, smiling and leaves the room, slamming the door behind her.


	10. Chapter 10

**Another Short one, but I promise another Chapter tomorrow after I have done at least 3 hours of studying for my exam. x**

Scully lies in her bathtub, fully clothed, gagged and bound. Skinner sits on the floor, head resting against the tub. Hands tied.

"I don't think its long now." He says, hearing Scully sniff back tears.

"Save the tears Dana, as long as I am alive I won't let them hurt you again."

X X X

Mulder walks along the corridor to his flat. He knows inside that they will be waiting for him. He hopes Holly is, he wants to know they have her, that they are going to take her back to wherever she came from.

Strughold meets Mulder at the door.

"We've been waiting."

He stands aside and lets Mulder walk in, the flat smells of smoke and sweat. Four men stand in the living room. Strughold closes the door and nods at one of the men.

The man leaves and a struggle can be heard.

"No, leave her, take me." Skinner shouts.

Scully is dragged into the living room by her hair, and thrown to Mulder's feet. He kneels and hugs her close, brushing her hair out of her face.

He pulls off her gag, and then hugs her close.

"I'm so sorry, Scully."

"It's not your fault."

"That's enough." Strughold interrupts, and one of the men pulls them apart, and puts Scully down on a seat.

Mulder stands.

"Now what?" Mulder glares at Strughold.

"Well, Mr Mulder, we tidy up. We just have a few more friends to wait for."

Strughold turns and walks over to sit on the arm of Scully's chair.

"Your children are both coming home."

Scully looks at him fear in her eyes.

"No, you're lying…"

"shhh…." Strughold smiles, putting his finger over her mouth.

"Don't touch her." Mulder rushes forward but is stopped by one of the men; he throws back onto the couch, and stands in between him and Scully.

Scully tries to control her breathing, refusing to look Strughold in the eyes. He leans down, and with his hand forces her head up. Scully eventually looks him in the eyes.

"That's better. I always wondered how someone so beautiful, could be trapped with a man so obsessed with other things."

Scully tries to pull herself as far back as she can from him. Mulder fidgets in his seat, he wants to charge, get Strughold away from her. Strughold stands and walks over to one of the men.

"Put Mr Mulder with Skinner."

"No!" Mulder starts to struggle, but one of the men handcuffs him, and pulls him away towards the bathroom.

"Scully! If you touch her, I'll kill you." Mulder screams, he is cut off as the door slams.

He turns to see Skinner.

"What's happening?" he asks.

"I was really hoping you'd be able to tell me."

Mulder sinks to the floor and sits by Skinner.

"I'm completely lost."


	11. Chapter 11

**Hopefully some questions answered in this chapter.**

Holly sits on a bench of a bus stop in the centre of small town. A rucksack sits in between her legs. A man walks over and sits beside her.

"Micheal." She gasps smiling and hugs him, he remains stiff.

"What the hell are you playing at coming here?"

Holly pulls back.

"I have nowhere else to go."

"And whose fault is that?"

"You're blaming me? He's the one that handed me over."

"I don't care; you've risked all of our lives even coming this close."

"William is miles away. How is he? Does he remember me?"

"He's fine. Let's go get something to eat and we can talk."

Holly follows Micheal to a small diner; they order food then sit in silence.

"I came back because this is where my family is."

Micheal doesn't respond and continues shredding his napkin.

"Talk to me, please."

"I don't know what you want me to say. We raised you for a year and a half, you were 15 when you left us, and now from what I hear you're a killer."

"That's what they trained me to be, but I'm not. I swear. I know I can't come back to stay with you, it's too risky I accept that, but I can have Scully. Can't I?"

"You stupid foolish girl, you had a family, you had Taylor, and he raised you well, and you threw that all away to be with them."

"That is a lie, he sold me to them, and I know what you'll say he did it to protect William, but if so he shouldn't have sent me to you in the first place, should he?!"

The waitress interrupts them, giving them both sandwiches. She smiles awkwardly and leaves them alone again. Holly refuses to look at Micheal. He rubs his temple.

"We loved you, if we'd know that it was the syndicate waiting for you, rather than Taylor, we never would have sent you. I promise. But I don't understand what you want now?"

"I spent three years of my life being experimented on, and trained to hurt and kill. They wanted me to get rid of all of them, Mulder, Scully, Skinner, Doggett, and even Reyes. But I can't kill her; she's my mum, no matter what they change about me. So they made me a deal, them for her."

"Holly, you couldn't have honestly believed they'd stand by it. Could you? Why are you here? You knew I wouldn't let you see William."

Holly sat she was thinking of the year and a half she had spent out here, looking after William, being part of a family. Dr Taylor had sent her after she discovered a photo of Scully and William, at 14 she had not fully realised what sending her would cost him. He had been her father in every way. Holly remembered the tears the day he called demanding she was dropped a mile from the airport, and walked to meet him there. She had done as told though; Micheal had warned her that staying would hurt William. But Taylor had never shown and instead she was taken away by Dr Foster, where years of pain began.

Micheal looks at Holly intently he can only guess at the thoughts in her head, the pain she has suffered.

"I don't know why I came here. I guess I wanted you to tell me what to do." Holly sighed, picking up her fork.

"You don't need me to tell you. You're gonna make this decision on your own; I trust you'll do what's right. Now eat up, and I'll drop you at the bus station."

Holly looked at him; she knew what she had to do. She always had. Holly and Micheal ate their lunch in silence.


	12. Chapter 12

Holly walked towards the bus station, she had made sure Micheal had come nowhere near here, and that he took a strange route home. Luckily his car had not been tagged. She could see them standing there, the large black car, Dr Foster, and three large men. She laughed to herself, was she really that much of a threat to them.

She walks up to them calmly.

"Hello."

Dr Foster smiled and opened the car door.

"Ready to come home at last. Where is your friend?"

"Long gone." Holly climbs into the car. Dr Foster climbs in and sits beside her, one of the men sits on her other side.

They sit in silence as the car pulls away.

"Can I ask one thing from you? I want to see her before I die." Holly says keeping her voice calm and controlled.

"Why would I make any deals with you? You are only seeing her as Strughold wishes it so. But in a few hours it'll all be over."

Holly sits silently as the car speeds up.

X X X

Scully lies asleep on her bed, she is not bound at all, but the marks on her wrists are clear. Mulder sits at the end of the bed. Skinner sits on a chair by the door.

"Why do you think they've untied us?" Skinner asks keeping his eyes on the door.

"I'd guess because they don't think we'll be around long enough for it to be an issue." Mulder sighs looking over his shoulder, to stare at Scully. He wants to wake her, just so he can talk to her, hold her, but can't stand the thought of disturbing her peace. He thinks suddenly of everything they could have had, a family, a home, happiness. All these things were never going to happen; he knew that they were going to make sure they never saw each other again. He was glad for this time though, being able to watch her sleep peacefully, in their bed, like nothing was wrong.

Skinner keeps watching the door; he can see the shadow of the man keeping guard. Scully begins to stir, turning over; she opens her eyes to Mulder leaning over.

"You okay?" he asks

"Yes, I'm fine Mulder."

She smiles, pulling herself into a sitting position carefully to make sure he can't see that every movement hurts, every inch of her body.

Mulder hugs her, she winces slightly, and he releases her. He looks at the massive bruise across her face, and wants to make all of them suffer.

"What's happening?"

Scully asks turning to look at Skinner.

"Not sure, we are just waiting for someone or something." Skinner sighs

Scully moves to sit on the edge of the bed with Mulder, leaning into him, his arm around her.

"Waiting it is then." She smiles at Skinner.

**Not really sure this is working how i wanted, but i promise i will finish it!**


	13. Chapter 13 (Penultimate Chapter)

**A short one, but only at penultimate chapter.**

Holly climbs out of the car; they are inside a small garage. The three men remain in the car, but Dr Foster climbs out. Dr Taylor appears from the shadow he is handcuffed.

"Holly." He says coldly

Holly stares at him. She turns to look at Dr Foster.

"Why is he alive? I put three bullets in his chest for a reason."

"He is an exceptional talented scientist; we couldn't just throw him away. But now that he has made it clear to us he will do no work for us, he's all yours."

Dr Foster hands Holly a gun, and leaves the room.

Holly and Dr Taylor stand in silence.

"You going to kill me then?"

"You want that don't you?" Holly spits at him.

"Yes! I want to die! I watched my own daughter butcher my girlfriend and son, and for what, because she was jealous, of all the…."

"No, don't you dare, you left me to be experimented on and abused by her, and anyone else interested in me."

Holly turns away, and Dr Taylor comes to stand behind her. Holly sensing his approach swings round and hits him with the butt of the gun. He falls back, staring up at her, Holly points the gun at his head.

"I used to worship you, and then I found out everything, she told me about the experiments, about how you handed me over for money. Rot in hell."

Holly puts off the safety on the gun.

"It's lies, please believe me, I did love yo….."

Holly shoots him dead. His body collapses, blood pooling around his head now marked with a star.

"I don't care"

Holly drops the gun and climbs into the car. Dr Foster enters a few minutes later, the car drives off.

"I was watching you know, I really didn't think you'd do it for a second."

"I'd rather I killed him, than one of your goons. Besides he's with his family now. As I will be shortly."

Holly closes her eyes, and leans back against the headrest. Dr Foster stares at her for a few seconds, trying to figure out what she is up to. She can't trust her; she barely knows what she is capable of.


	14. The End

Scully, Mulder and Skinner sit on their knees, hands tied, bags over their heads. Holly, Dr Foster and one of the men enter the flat.

"Is that really necessary?"

Holly sighs sitting on the sofa.

Strughold smiles.

"Of course not, just a little fear tactic, we got bored waiting."

He nods at two of the men, who remove the bags from their heads; Strughold meanwhile goes and sits beside Holly. But she stands up, and goes over to Mulder.

Mulder looks at her, eyes filled with anger.

Holly bends down as to be eye level with him.

"I'm sorry about this."

"A bit late for apologies." He hisses

"I wasn't talking to you." She smiles

She turns and punches one of the men, sending him reeling backwards; she reaches and grabs his gun. His friend lunges towards her and she shots him dead. The initially man grabs her by the hair, and she shots him in the gut.

She then turns her attention to Dr Foster, who is cowering behind the other three. Holly breathes in, the three men all have guns trained on her. She concentrates and fires. She misses Foster, and instead hits the wall. The three men, disarm her quickly, forcing her to her knees, and begin to handcuff her.

"Wait!" Dr Foster commands, and marches over to Holly, forcing her head up, with her hand around her neck.

"What the hell were you thinking? You really thought that you could kill me that easily."

"I wasn't thinking I was just fuelled by hatred like you taught me."

Dr Foster turns away.

"Don't bother handcuffing her, let's get this over with."

Holly smiles, and reaches into her converses, and pulls out a knife, before, the men can react, Holly throws it. It slices through the flesh and bone of her neck, Dr Foster falls gasping. The point of the blade is just appearing through the front of her neck.

Dr Foster lays gasping, pain shooting through her body.

"I wanted you to suffer in your death; I hope you are thinking about all my siblings and…."

One of the men hits her round the head. Holly crumples, white pain, fuzzing her brain.

Holly's vision starts to come into focus, and she is aware of someone saying her name.

She forces open her eyes, to see Scully leaning over her.

"You're alright," Scully says, she stares at Holly. Who quickly sits up, and surveys the room.

Dr Foster's body is gone, as are those of the two men.

"You've made this a lot messier than it should have been. Luckily we have time."

"How? Martin Walsh's body must have been discovered by now."

"Oh, it has, just, see he had asked not to be disturbed all day, so the cleaner found his body an hour or two ago."

"Why aren't the police here?"

"We've sent them on a wild goose chase, but they will be soon."

Holly stands, Scully follows her lead.

"What are you going to do?" Scully asks

"You want to reveal the plan?" Strughold laughs, he walks over to Scully.

"I'm going to miss you the most."

Strughold lights a cigarette and then nodding at the men leaves the flat.

Holly turns to look at the men, me against 3 of them easy, she smiles.

One of the men grabs Scully and stands with her in front of him, gun pressed to her head.

"Just in case, you decide to fight." The man smiles at Holly.

One of the other men, puts on gloves, and pulls out Mulder's gun.

"Framing me, I see."

Mulder asks, standing, he wants to be by Scully. Skinner remains kneeling, one of the men stands behind him, and he fears that trying to stand will just result in pain.

The man behind Mulder pulls out his gun keeping it trained on Mulder, as he makes his way over to stand opposite Scully.

Mulder punches the man holding Scully, knocking the gun out of his hand. The gun falls to the floor, the two men dive for it, fighting. A shot goes off, Skinner falls blood pooling around his body.

Scully screams, and runs to Skinner, holding him in her arms, crying. Skinner tries to speak, but blood splutters out his mouth instead.

In the confusion, Holly knocks out the other man, taking his gun, and shooting him in the head. She turns, to see Mulder bleeding, the man in the suit standing over him with a gun.

"You have to pick Holly." He laughs, his lip is bleeding. He kicks Mulder in the stomach, Scully screams out.

"No stop it!"

The man behind her presses a gun to the back of her head.

"Who's gonna die first Holly?"

"Stop playing with her." The man behind Scully commands, turning to look at his partner.

Holly in the second he is distracted shoots him. She points the gun at the last man.

"Think your fast enough?" she asks her eyes cold.

They both fire. Both of them fall. The man dead, shot through the head.

Mulder sits up, and comes over to Scully. She unties his wrists.

"Call an ambulance."

She carefully lays Skinner on the floor. Squeezing his hand and goes over to Holly. She has been shot in the stomach, she lies gasping for air.

"You have to make sure I'm alive when the police arrive, I have to confess."

"Shhhh." Scully says moving Holly's hair out of her face.

"You're not on any cctv in the FBI, I made sure." Holly gasps, as Mulder talks to the emergency services.

Scully applies pressure to the bullet wound.

"You know I always hoped to die like this."

Scully looks away tears forming.

"You know surrounded by people I've killed." Holly laughs, and then coughs.

Scully looks at her smiling in sympathy.

"Don't feel sorry for me, I like to think that I did something right. Keep talking to me."

Scully nods

"You did, you saved us."

"I know William. He's beautiful, and kind, the most pure and loving child you could ever imagine. And his family love him."

Scully cries, Mulder comes over and puts his arm around her.

"Thank you."

Holly nods.

"I always imagined when I died I'd be back with my siblings, and my family. But with all the evil I have done, I know I'll be in hell with Foster. Just what I deserve."

Scully pulls Holly close.

"No, you are good. I'm proud to be your mother."

Holly turns her head away trying to hide her tears, pain pulsating throughout her entire body.

X X X

Scully stands in the corridor outside the apartment, still covered in blood, Mulder comes out and hugs her.

A gurney with a body bag on it exits. A FBI agent follows it out.

"That's all the evidence we need collected. I'm sorry for your loss."

He nods and they all leave, closing the door, behind the police tape.

"Let's get out of here, for good. Let's go and buy a house in the country, be can do this now, Holly has made it possible."

Mulder looks at Scully, arms wrapped around her.

"Yes, I want that more than anything." Scully smiles and they share a deep kiss. And they leave together.

Epilouge

Holly lies on an operating table, covered with a sheet.

Her eyes suddenly open and she gasps.

Strughold stands in the corner of the room.

"Evening."

**Hey thanks for sticking with me. Hope ending ain't disappointing. Please Review! Thanks x**


	15. Sequel

Was thinking about doing a sequel, so please review and let me know if I should. x

Sequel is now up! The Spy in the Campaign.

Hope you like it. x

xxx


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